6NDN | pdb_00006ndn

Crystal Structure of Selenocysteine Lyase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb6NDN/pdb

• Classification: LYASE
• Organism(s): Escherichia coli UMEA 3718-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-14 Released: 2019-12-25 
• Deposition Author(s): Scortecci, J.F., Brandao-Neto, J., Pereira, H.M., Thiemann, O.H.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Selenocysteine Lyase from Escherichia coli

Scortecci, J.F., Brandao-Neto, J., Pereira, H.M., Thiemann, O.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.74 kDa 
• Atom Count: 3,588 
• Modeled Residue Count: 406 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	A	406	Escherichia coli UMEA 3718-1	Mutation(s): 0  Gene Names: sufS, G994_01747 EC: 2.8.1.7 (PDB Primary Data), 4.4.1.16 (PDB Primary Data)

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.52	α = 90
b = 126.52	β = 90
c = 134.091	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Scortecci, J.F., Brandao-Neto, J., Pereira, H.M., Thiemann, O.H.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2016/20977-7

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description